


Not What They Thought It Was

by NightDoktor



Category: The Maze Runner (Movies), The Maze Runner Series - All Media Types, The Maze Runner Series - James Dashner
Genre: Eventual Smut, F/M, Fix-It, Flare strains are unique, Fuck Canon, M/M, Newt Lives, Newt is stubborn as hell and refuses he has the gay, People can develop the same Flare strains, The Flare is a curse, explicit for language and smut scenes, fantasy/magic, immune!newt, one sided Aris/Thomas
Language: English
Status: In-Progress
Published: 2018-02-02
Updated: 2018-02-04
Packaged: 2019-03-12 13:26:04
Rating: Explicit
Warnings: Creator Chose Not To Use Archive Warnings, Graphic Depictions Of Violence
Chapters: 2
Words: 3,951
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/13548267
Author URL: https://archiveofourown.org/users/NightDoktor/pseuds/NightDoktor
Summary: The Flare was not what they thought it was. Instead, it punished those not strong enough to host it.The Flare has mutated well beyond what humanity thought possible. Now, those Immune must learn to control it, or WICKED will.





	1. Prologue

The boy knew the world was dying, if not already dead. Scorched, killed, it’s humanity succumbing to a disease that was unleashed without knowing where it came from, what it was capable of, or how it would evolve. Only that it was an act of war, to reduce the number one inevitable problem: population.  
He knew this, and only this, as he grabbed onto the sides of the steel box he found himself in, knuckles white with fear; of both the unknown and the vertigo.

When the box stopped, his head spun for a few moments, and the sounds of it opening were all too loud. Blearily, the boy opened his eyes and peered out, making out the silhouettes of a group of people, all talking amongst themselves in hushed whispers, afraid he’d hear what they were saying.  
A rope was thrown down into the box, and he recoiled when it hit him, though quickly gathering the point of it and clambering out of the box, only to whirl around, taking in the crowd of boys, all around his age, and the harsh mix of concrete structures and rough wooden ones.

As one tried to approach, his mind froze.  
_Thomas._  
With a strangled cry, a black mist wrapped around his forearms, thick black veins shooting across his skin, and threw back the boys around him. Thomas ran through the gap, panting and screaming as the black mist and the veins retreated with his remaining strength, and he collapsed.

**Notes for the Chapter:**

> This is just a short teaser of what I have planned. 
> 
> My first Maze Runner work, and I hope to make it epic length, until the end of the plot. I haven't read the books, but I will be doing so to try blend book and movie as much as I can.
> 
> Peace out!


	2. Awakening

**Summary for the Chapter:**

> Thomas wakes, and has his first few days in the Glade.

His wrists _hurt_. It was the first thing that registered, followed by a thundering ache in his head, and a dull, deep thumping of pain in his shoulders.

He slowly managed to open his eyes, stinging from the light in the small room he was kept in. They’d at least put some blankets underneath him first, he noticed.  
Muffled, voices floated in through the gap around the door.

“I’m tellin’ ya, his arms had the Flare markings all up them before he used it to knock all of us back. It’s a Strain. I’m sure of it.” That voice, it had to be Newt.  
“If you’re sure, you’d know about it. Have you used Mind Web to look into him yet?” a deeper, slow voice replied in question.  
After some silence, Newt replied something in a low tone that Thomas couldn’t hear, followed by a heavy set of footsteps thumping, growing fainter with the distance.

Thomas’ wrists burned, and he anxiously tried to move his shoulders, instantly regretting it. It was all he could do to keep the yell of pain within, as his shoulders came to life very painfully.  
It was after a wait that seemed to burn as much as his limbs, that Newt slowly opened the door to peer in cautiously.

“Not going to throw me halfway across the buggin’ Glade are ya, Greenie?” Newt asked, hiding behind the door as if it was going to offer any shelter from a supernatural energy wave.

Thomas cocked his head to the side, and offered a single, intelligent, “Huh?” in response.

Newt, now confused, stepped into the room, closed the door and crouched in front of the bound boy. Thomas froze, and memories flashed before him. Coming up in the cold unforgiving Box. Being surrounded and overwhelmed by people, talking, shouting and faces. So many faces. He remembered the surging feeling of forboding as it gripped him, and he shoved the people away, so he could run, then nothingness.

“I remember yesterday.” He croaked, clearing his throat and gratefully drank the water Newt retrieved.  
“Okay Greenie. This is how it’s going to work. I’m going to enter your mind, and you’re not going to do a buggin’ thing about it. Good that?” Newt stood, hands on hips, expectantly waiting.

Thomas’ eyes narrowed. “You’re going to what?”

“Oh, shuck this.” Newt sighed, dropping onto his knees and awkwardly sitting on one of his legs, the other bent out at an awkward angle.  
He then reached out, and touched Thomas’ forehead, black veins crawling up his arm, and his eyes going as black as night, Thomas’ eyes doing the same, indicating a perfect connection.

Newt stood in a sea of stars, clothed in nothing but a swarm of light. He walked forwards, and started talking, but they weren’t words he uttered. He released thoughts, memories, visions, his being.  
Eventually, a manifestation of Thomas appeared, similarly clothed in light. He too, released thoughts, feelings, his being, having been bound by a force of Newt’s power. Equivalent exchange.

Thomas blinked, and fell backwards onto the sheets, dazed and struggling to process the influx of memories and thoughts.  
Newt coughed, gathered himself and stalked out of the room, angrily rejecting the return information that Thomas’ subconscious had been compelled to give. His ability worked like that; if he didn’t control the flow, a balance must be maintained.  
Grunting, his feet brought him to the track-hoes, where he wordlessly grabbed a small shovel and got to work, fitting in seamlessly around the others.

-

The room was lit with a rich orange glow when Thomas awoke again. This time, his limbs were unbound, and he had no recollection of who had cut his bonds, nor when. Gratefully flexing his limbs, regaining feeling once more, he gingerly stood and took a few test steps.

Satisfied that he could at least walk, he slowly opened the door and peered outside, similar to how Newt had used it for shelter hours before. Finding no one in the vicinity, Thomas wandered until he found his way out, and took time taking in the sight of a few people around a small fire.

Noticing Newt before anyone else, he took his time walking over, and tentatively sat down, avoiding strain on any sore joints.  
“How you feelin’, Greenie? Newt have a good time rearranging the furniture in there?” Alby asked, giving himself a short guffaw at his own joke, before rising to his feet with a grunt.  
Not giving time for Thomas to reply, he tasked Newt with showing the Greenie the Wall, and went off to yell orders at some boys slacking off.

Newt side eyed the boy beside him, and sighed. “Whatever you think you got from me, think very carefully before you ask any dumb questions, got it Greenie?”

Thomas mutely nodded, and raised his hands in surrender. “Got it. So, what’s the Wall that Alby talked about?”  
Newt grew serious, and cast his eyes aside. “Let’s go show you then, I s’pose.”

Thomas shot to his feet a little quickly, but recovered in time to offer Newt a hand. The other boy eyed him warily, before getting up well enough on his own, and walking past Thomas.  
“Come on then, don’t be off staring at the dirt.”  
Thomas shook his head roughly to wake himself from staring at the spot Newt had sat, his dark eyes regarding him as if he could see right through him.  
_Which, he did, I guess._ Thomas mused, turning and following the blonde through the Glade.

After some time, the pair arrived at a section of the maze wall, with names carved into its surface. Some, Thomas noted with a sinking feeling, had been scratched out.  
“Now you’re one of us, it’s time to learn what you want to know. Think through what memories I imparted to you, and listen carefully. The Flare kills those via attacking the brain that aren’t immune. If you are, the Flare mutates into a strain, and each strain gives a new ability. So far, we haven’t seen anyone with the same strain yet, so you get to name it, once you work out what it does.” Newt explained, Thomas deep in thought over all the information Newt had imparted to him via their mental link earlier.

Stepping forward, Thomas focused on the feeling of dread that now sat, unmoving, at the back of his mind. He recalled from Newt’s memories that it was the Flare’s power, waiting to be tapped into. He reached, and grabbed a hold of it.  
He focused on his index finger, and the Flare markings crawled up his body, and up his arm, when the black mist condensed around the tip of his finger, forming a wicked claw.  
Walking slowly out of respect for the dead, Thomas carved his name near Newt’s, and watched as the carvings smoked black for a few moments before settling. He released the energy around his finger, and stepped back to glance at Newt, who nodded and turned on his heel, walking towards the Homestead again.

On the way, Thomas mulls over more memories he received from Newt. The Gladers had received basic information about the Flare, but the rest, they’d assembled through conjecture. He’s called out of is reverie when Newt calls out to him, already quite far ahead.  
Thomas snaps back to reality, and runs to catch up with the blonde.  
“So, Greenie, you’re the star tonight. We put on a bonfire each month to celebrate the new arrival, and tonight that’s you.”  
Thomas startled. “Wait, what?”  
Newt just smiled before shoving him towards the bonfire. The next few hours went by in a blur. He wrestled with Gally, talked incessantly with Zart, and laughed with Chuck.  
It was towards the end, when the younger Gladers were getting in bed, that Thomas found himself leaning against a log they’d used as a seat next to Newt.

The blonde offered Thomas a jar, with a funky liquid in it.  
“Go on, it’s Gally’s secret recipe. He only makes it for special occasions.” Newt proffered the jar, and grinned when Thomas took it, sniffing it warily.  
“Go on ya shank, drink it!”  
Thomas couldn’t help but choke and spit it everywhere, as the rancid liquid hit the back of his throat, and had to look away and hiss to ignore Newt’s rambunctious laughter, which drew the attention of many people. Once they worked out what it was, they also laughed and went about their night, occasionally pointing back to the Greenie.

Once Newt’s laughter died down, Thomas took a good look at Newt.  
The boy was not that much taller than he was, with golden blonde hair that was alight in the firelight, which likely had never known order, eyes as dark as the night sky, but Thomas was sure they were a lovely shade of dark brown, the most perfect nose and these soft, pink lips that were accompanied by a jaw Thomas imagined running his fingers along…

He shook his head and stared at the fire instead. It was not going to judge him, after all.  
“You alright, Greenie?”  
Thomas huffed. “My name is Thomas, Newt. Did you forget already, ya shank?”  
He side eyed the blonde as he turned to face Thomas, amusement lit clearly in those eyes.  
“You’re getting the hang of it. Hmm… I’ll call you Tommy. Suits you better, I think.”  
Thomas couldn’t help but blush at the nickname, and swore to never let anyone else call him that.  
“Newt, with the memories you showed me-”  
“Thomas. I told you not to speak of them, didn’t I?” Newt cut him off roughly, before standing.  
“Newt, hear me out. Perhaps it was something with the connection, but I feel like I know you. You’re such a genuine self-sacrificing person, and I really do think you need to let yourself have time to grieve. I don’t want you to be alone. You’re isolating yourself and you know it!” Thomas rose too, and touched Newt’s arm.

Newt pulled away with a growl, and glared over his shoulder at Thomas, hurt in his eyes.  
“Don’t buggin’ talk to me as if you know me at all. Stay out of what doesn’t concern you and do what you’re told.”  
The blonde stalked off to the Homestead, not to return that night. Defeated, Thomas flopped against the log, and sulked.

“Newt isn’t the easiest shank to talk to, but I don’t suppose you’d know that, or listen to me if I’d have told you, eh?”  
The voice shocked Thomas out of his musing, and he looked up to see one of the Runners before, the Keeper, to be precise, complete with perfect black hair, and Asian appearance.  
The Keeper walked around beside Thomas, and was careful to sit on the opposite side to where Newt had sat.  
“Name’s Minho, and I’m the Keeper of the Runners. We usually go out into the Maze, see what changes and all that and come back before dusk, when the doors close.” Minho explained, offering his hand.  
Thomas gripped it firmly. “Thomas. I think Alby already has a plan for me tomorrow, but I sincerely doubt that includes me out there.”  
Minho let out a laugh. “Of course, ya dumb shank! You’re chosen for a Runner, you don’t choose to be a Runner. Give it time.”

Thomas went to his hammock that night with a heavy head, and slipped into a dream with only Newt’s back turned to taunt him.

-

Chuck woke him up the next morning, and wouldn’t cease his chatter until Thomas swatted at him to move, so he could extract himself, with no small amount of difficulty from the hammock.  
Frypan served up breakfast with his usual gusto, and Chuck slowly woke Thomas up with a serving of chatter to match the serving of breakfast.  
It wasn’t soon after he’d finished that Alby came for him, and assigned him to the Slicers until lunch.

After hours of barely holding back his breakfast, Thomas stumbled out of the makeshift abattoir, gulping in the fresh air.  
Lunch was a short affair, when he was then assigned to Gally’s section, the Builders. He was mostly shoved out of the way, and assigned to menial tasks, as they didn’t want him around. Gally watched him like a hawk, but didn’t disapprove of his work, which Thomas quietly celebrated.

He watched with no small amount of jealousy as Minho and Ben returned from the Maze, bringing their sprint down to a slow jog as they debriefed with Alby.  
Thomas grunted as he picked himself up from the fire, trying to find Newt. Sighing when he couldn’t find the blonde, he decided to turn in for the night.  
Clambering into the hammock, Thomas craned his head to peek at the tips of the Maze walls that kept them bound in the Glade. He turned his thoughts inwards, to the Flare, which waited patiently at the back of his mind, waiting to be released again. He felt the desire to unleash it, to ride out the wave of power, but knew he would not last more than 5 minutes if he did so.

It was able to manifest his thoughts into reality, right? Manifestation. Keep it simple. Thomas grinned at the genius of the idea, and couldn’t wait to tell Newt. If only, he’d talk to him. Thomas frowned when he recalled it’d been a day since he’d even seen the other boy, let alone talked to him. He wondered if he was okay.

-

He’s shaken awake again, and Thomas gasps, and nearly throws himself out of the hammock and onto the ground.  
Thomas collected himself and his bearings, before meeting a bemused Newt, who put his finger to Thomas’ lips before he could speak.  
“Slim it. Come with me, I need to show you why you should fear that buggin’ Maze.” Newt breathes, before turning and leisurely walking away, his limp barely noticeable.  
Thomas trips over his own feet, barely avoids a sleeping Glader and nearly ends up face first into another. Gaining his balance again, he tiptoes through the mess of bodies and hammocks before coming to a stop behind Newt, who’d arrived at a vine infested section of the wall.  
“I was afraid we’d miss it, with your slow ass.” Newt informs him blithely, stepping to the side, parting the vines with his hand.  
“Go on, look. Don’t look away until you see it.” Newt yawned, already looking at the Glade, planning what needed to be done that day.

Thomas peered into the vines, before seeing a transparent section of the wall. He hums, lips pursed. What’s there to see? Thomas wondered, before launching himself backwards with a strangled cry.  
In the window, was a bulbous, clawed creature with bright red eyes. It scratched at the window, before moving on.  
Newt made his way over, and looked down at Thomas with a disinterested frown.  
“And that, Greenie, is why you’re not going anywhere near that buggin’ Maze. You’ll end up a pile of klunk that we’ve just gotten to know and tolerate.” He sighs, and offers Thomas a hand.  
He gratefully takes it, and doesn’t let go for a moment longer than what was normal.  
“Newt, I’m sorry about the other night at the bonfire. I didn’t want to scare you off or make you feel like that. I want you to know because of that connection, I’d be someone who understood. That’s all.” Thomas babbled, voice falling flat at the end, eyeing Newt carefully in case he bolted again.  
He opened his arms, and slowly embraced the blond.  
Newt let out a soft sound of surprise in this throat, but didn’t pull away. He let his head fall onto Thomas’ shoulder.  
“You’re forgiven. Now, slim it,” he pulled away, and crossed his arms with a smirk, “you’re on track-hoe duty with Zart until lunch, then we’ll set you up with Frypan a few hours after, for dinner.”  
Thomas mock salutes, and almost skips away, heart ten times lighter than it was the previous day.

Newt hangs behind, and scowls at himself when he finds the lack of warmth uncomfortable, and rather enjoyed the contact. _What the shuck is this?!_

-

Thomas watches Minho and Alby run off into the Maze, and recalls with a cold shiver the Griever that he’d seen just moments before, but is calmed by the memory of holding Newt close to him. _Ugh. Of course. I’d forgotten, that I wasn’t straight. Fuck._ He cursed to himself, before stalking off to the galley to get a meal from Frypan and his crew, making sure to mention he was going to be working with them for dinner that night. Frypan mock saluted, before telling him to “shuck off, I’ve got mouths to feed!” so Thomas scarfed down his food, rather excited to be working with Zart.  
He’d managed to talk to the Keeper for a while on his bonfire night, and he got on quite well. He might be able to help with his Newt problem.

A couple hours in, Thomas rocked back on his heels in a squat, taking a few minutes break. Digging repeatedly turned out to be quite tiring.  
He turned to Zart. “Hey Zart, about Newt…”  
The Keeper eyed him for a few moments, and nodded. “What about him?”  
Thomas swallowed, hoping to keep the rising blush from his face as he spoke about his… _crush_?  
“When I got here, he entered my mind and we exchanged thoughts and memories. Ever since he’s been really hard to talk to and won’t let me in, to talk about what I saw.”  
Zart considered it for a while. “I’ve known Newt for a good lot of time now, and he’s never been one to spill emotions. It’s not necessarily a bad thing here, we all gotta help each other. Just he’s very set in maintaining his role as second-in-command, and to him that means being strong at all times, so the boys can look up to him as well as Alby.”  
Thomas fell onto his butt, and huffed in resignation. “I guess.”  
Zart winked, and tried to hide a grin as he went back to planting seeds. “Work while you talk, Greenie. We don’t have all day.”  
Thomas laughed, but went back to work nevertheless.  
“Newt’s ability is Mind Web. It allows him to link many peoples’ minds together at once, but he can also turn that on just one person. He should be able to do one-way transfers of memories soon, but he hates doing it because he becomes vulnerable when people learn too much. He’s probably still dealing with that, or what he felt coming from you.” Zart explains, eyeing off said blonde in the distance, sorting out a squabble as a mediator.  
“I’ll keep your little crush on him a secret for now, but I can bet my favourite shovel that he’d know about it and refuses to even consider it. Give him time, Thomas.” Zart winked, and laughed as Thomas spluttered and indignantly denied it.  
“Oh please, we can all see the way you look at him, and we also see the side glances he takes when he thinks no one is watching.” Zart snorts, and goes back to planting, leaving Thomas blushing up to his ears, and nothing to say in reply.

Lunch rolls around soon enough, and after talking more with Chuck and Zart, he finds Newt perched on a tree stump near the Maze entrance.  
Thomas perches himself next to Newt, and offers him his share of the sweets. Newt declines, but gives a small smile instead.

“Newt, I got Zart to explain a bit today. He explained how your Strain works, and I feel dumb for not asking you yourself about it. How did you awaken it? Thomas asks, keeping a careful eye on the blonde, who tensed at the question.  
“I had… an incident, in the Maze, when I was a Runner. I’d linked the whole Glade, and they worked out where I was, with all of the shanks shouting in my head. Next thing I knew, I was in the Homestead, barely alive.” Newt explains, rubbing the back of his head at the memory.  
“Seems you didn’t get that one when we first met, then.” Newt surmises, glancing at Thomas, who shook his head.  
“I’ve gotta get going with the Cooks, see you around Newt.” Thomas gripped Newt’s shoulder gently, giving a smile as he left.  
“Thanks, Tommy.” Newt mumbled, suddenly fixated on the doors, and found something interesting to stare at.  
Thomas grinned widely, and practically skips off to find Frypan.

-

Dusk had settled, and Thomas noted with some alarm that Minho and Alby aren’t back yet. He dumped his washing in the large bucket, and flings his apron back into the mess before joining Newt at the Doors.  
“Newt, where are they?” Thomas asked, voice rising slowly with his fear.  
Newt didn’t respond, instead resolutely looked down the corridor, waiting hopelessly for the dumb shanks to round the corner.

They did, but only as the doors started their inevitable shift closed. Minho was lugging a nearly unconscious Alby, but it was obvious they wouldn’t make it in time.  
Just as the doors allowed, Thomas lurched forward, Newt grabbing at empty air to try and stop him. He got to the doors, and panicked, reaching within himself and dragged that dread forward, eyeing the black veins and blacker mist that ghosted around his hands.  
He formed a long cylindrical shape, steadied it with his hands, and locked it in place to prevent the doors closing. A deep groaning sound of gears echoed from the ground, and Newt shouted out something, but Thomas couldn’t hear over the sound of blood rushing through his head.

He roared with the exertion, and watched with sweat beading down his face as white cracks formed in his manifestation, spiderwebs of light making their way over the object, and shattering with a dull thud as the doors slammed shut, Minho and Alby on the floor beside him.

A moment later, Thomas saw black as he joined them on the floor, dully registering Newt barking orders.  
_Newt…_

**Notes for the Chapter:**

> So, Chapter One is up.
> 
> It's taken me a while to flesh out how I'm going to try and make this as canon-compliant for a while, and incorporating my idea of the Flare into it, so it might be some time before another update.
> 
> Peace out!


End file.
